In an earlier question/answer you said that colored illustrations are not a good idea le’chatchilah on a Haftorah scroll, but be’di’eved their presence would not make the scroll unkosher.
See attached picture.
Therefore, can the illustrations only be covered with blank klaf during a reading
It will help it partially. There are two issues with having the pictures in the megillah. The first is that preferably it should be like a sefer torah, where it is not permitted for anything to be added, secondly, the pictures disturb the person’s concentration. Covering the pictures will help for the second reason but not for the first.